Incidence of Treatment Emergent Serious Adverse Events by Treatment Group

The reference report's Table 14-5.02: the serious treatment-emergent events, counted and tested the same way as the full incidence table.

Slug: t-sae-incidence
Regulatory ID: AET04
Type: Table
E3 position: §14.3.2
Status: evidenced
Current iteration: v006
Datasets: adae 4ffe4e4, adsl 3139478
Evidence: 25/25 passing
Requirements: DSP-AEI-001 DSP-AEI-002 DSP-AEI-003 DSP-AEI-004 DSP-ALL-001 DSP-ALL-002 DSP-INTXT-001 DSP-INTXT-002 DSP-INTXT-003 DSP-REF-001 DSP-REF-002 DSP-REF-003 DSP-REF-004 STD-GATE-001 STD-GATE-002 STD-GATE-003 STD-GATE-004 STD-GATE-005 STD-MODEL-001 STD-MODEL-002 STD-MODEL-003 STD-MODEL-004 STD-MODEL-005 STD-SRC-001 STD-SRC-002
Used in: Clinical Study Report Table 14.3.2.2
Post-Text Display Package Table 14.3.2.2
Abbreviated Clinical Study Report (ICH E3) Table 14.3.2.2
Study model: Safety Analysis Set SAFFL · grouped by TRT01A
Specification: 6 iterations
Environment: R 4.3.3 Darwin 23.6.0
Bound by: No text block binds it
Values: No value is sourced from it

Inputs

adsl254 rows · 3139478
adae1191 rows · 4ffe4e4
analysis.yamlwhat to compute
display.yamlhow to show it
study modelSafety Analysis Set

Function

prepare_data()regenerate('t-sae-incidence')
build_ard()one row per statistic
render_display()every variant
render_rtf()the same cells

Outputs

ard.jsonv006 · 64 rows · 94a983c
table.htmlthe rendered display
table.rtfsha256 4586728
table-in-text.rtfsha256 36aafe2
manifest.jsonwho, why, every hash

RTFFull display4586728 RTFIn-text variant36aafe2

Generated by the same pipeline run that wrote the ARD and the HTML above, from the same rendered cells; the short hash is the manifest's record of the file.

t-sae-incidence · post_text variant · study CDISCPILOT01 · data cut-off 2014-07-01

	Placebo (N=86)	Xanomeline Low Dose (N=84)	Xanomeline High Dose (N=84)	Placebo vs. Low Dose	Placebo vs. High Dose
Incidence of Treatment Emergent Serious Adverse Events by Treatment Group
Study CDISCPILOT01 — Safety Analysis Set
ANY BODY SYSTEM	0	1 (1.2%) [1]	2 (2.4%) [2]	0.494	0.243
NERVOUS SYSTEM DISORDERS	0	1 (1.2%) [1]	2 (2.4%) [2]	0.494	0.243
SYNCOPE	0	1 (1.2%) [1]	1 (1.2%) [1]	0.494	0.494
PARTIAL SEIZURES WITH SECONDARY GENERALISATION	0	0	1 (1.2%) [1]		0.494
Serious treatment-emergent events are those flagged AESER = 'Y' and TRTEMFL = 'Y' in the study's ADAE, as the reference report (Table 14-5.02) counts them. Adverse events are coded using MedDRA.
Subjects are counted once per system organ class and once per preferred term; percentages are based on the number of subjects in the safety population within each treatment group. The bracketed figure is the total number of times an event was recorded.
P-values are Fisher's exact test comparing placebo with each active treatment group on the number of subjects with the event. An asterisk is appended to p-values below 0.15, as in the reference report; a p-value that rounds to 1 prints as >0.99; where neither arm has a subject with the event there is no test and the cell is blank.
System organ classes are in alphabetical order; preferred terms within a class are in descending order of subjects across the three groups, then alphabetical — the order the reference report's serious-events program prints, which differs from its full incidence table.
Source: adae, adsl (CDISCPILOT01 ADaM package, phuse-org/phuse-scripts). Data cut-off: 2014-07-01.
open.csr display t-sae-incidence (post_text variant); generated from the committed ARD.

Rendered from outputs/t-sae-incidence/v006/table.html.

analysis	group1	group1_level	group2	group2_level	variable	variable_level	context	stat_name	stat_label	warning	error	stat
any	TRT01A	Placebo	—	—	ANY	—	subject_count	n	n	—	—	0
any	TRT01A	Placebo	—	—	ANY	—	subject_count	N	N	—	—	86
any	TRT01A	Placebo	—	—	ANY	—	subject_count	p	%	—	—	0
any	TRT01A	Placebo	—	—	ANY	—	subject_count	events	Events	—	—	0
any	TRT01A	Xanomeline Low Dose	—	—	ANY	—	subject_count	n	n	—	—	1
any	TRT01A	Xanomeline Low Dose	—	—	ANY	—	subject_count	N	N	—	—	84
any	TRT01A	Xanomeline Low Dose	—	—	ANY	—	subject_count	p	%	—	—	0.0119047619047619
any	TRT01A	Xanomeline Low Dose	—	—	ANY	—	subject_count	events	Events	—	—	1
any	TRT01A	Xanomeline High Dose	—	—	ANY	—	subject_count	n	n	—	—	2
any	TRT01A	Xanomeline High Dose	—	—	ANY	—	subject_count	N	N	—	—	84
any	TRT01A	Xanomeline High Dose	—	—	ANY	—	subject_count	p	%	—	—	0.0238095238095238
any	TRT01A	Xanomeline High Dose	—	—	ANY	—	subject_count	events	Events	—	—	2
any	statistic	Placebo vs. Low Dose	—	—	ANY	—	hypothesis_test	p_value	Fisher's exact p-value	—	—	0.494117647058824
any	statistic	Placebo vs. Low Dose	—	—	ANY	—	hypothesis_test	p_value_fmt	Fisher's exact p-value (formatted)	—	—	0.494
any	statistic	Placebo vs. High Dose	—	—	ANY	—	hypothesis_test	p_value	Fisher's exact p-value	—	—	0.242673163940132
any	statistic	Placebo vs. High Dose	—	—	ANY	—	hypothesis_test	p_value_fmt	Fisher's exact p-value (formatted)	—	—	0.243
by_soc_pt	TRT01A	Placebo	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	n	n	—	—	0
by_soc_pt	TRT01A	Placebo	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	N	N	—	—	86
by_soc_pt	TRT01A	Placebo	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	p	%	—	—	0
by_soc_pt	TRT01A	Placebo	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	events	Events	—	—	0
by_soc_pt	TRT01A	Xanomeline Low Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	n	n	—	—	1
by_soc_pt	TRT01A	Xanomeline Low Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	N	N	—	—	84
by_soc_pt	TRT01A	Xanomeline Low Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	p	%	—	—	0.0119047619047619
by_soc_pt	TRT01A	Xanomeline Low Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	events	Events	—	—	1
by_soc_pt	TRT01A	Xanomeline High Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	n	n	—	—	2
by_soc_pt	TRT01A	Xanomeline High Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	N	N	—	—	84
by_soc_pt	TRT01A	Xanomeline High Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	p	%	—	—	0.0238095238095238
by_soc_pt	TRT01A	Xanomeline High Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hierarchical	events	Events	—	—	2
by_soc_pt	statistic	Placebo vs. Low Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hypothesis_test	p_value	Fisher's exact p-value	—	—	0.494117647058824
by_soc_pt	statistic	Placebo vs. Low Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hypothesis_test	p_value_fmt	Fisher's exact p-value (formatted)	—	—	0.494
by_soc_pt	statistic	Placebo vs. High Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hypothesis_test	p_value	Fisher's exact p-value	—	—	0.242673163940132
by_soc_pt	statistic	Placebo vs. High Dose	—	—	AEBODSYS	NERVOUS SYSTEM DISORDERS	hypothesis_test	p_value_fmt	Fisher's exact p-value (formatted)	—	—	0.243
by_soc_pt	TRT01A	Placebo	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	n	n	—	—	0
by_soc_pt	TRT01A	Placebo	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	N	N	—	—	86
by_soc_pt	TRT01A	Placebo	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	p	%	—	—	0
by_soc_pt	TRT01A	Placebo	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	events	Events	—	—	0
by_soc_pt	TRT01A	Xanomeline Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	n	n	—	—	0
by_soc_pt	TRT01A	Xanomeline Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	N	N	—	—	84
by_soc_pt	TRT01A	Xanomeline Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	p	%	—	—	0
by_soc_pt	TRT01A	Xanomeline Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	events	Events	—	—	0
by_soc_pt	TRT01A	Xanomeline High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	n	n	—	—	1
by_soc_pt	TRT01A	Xanomeline High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	N	N	—	—	84
by_soc_pt	TRT01A	Xanomeline High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	p	%	—	—	0.0119047619047619
by_soc_pt	TRT01A	Xanomeline High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hierarchical	events	Events	—	—	1
by_soc_pt	statistic	Placebo vs. Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hypothesis_test	p_value	Fisher's exact p-value	—	—	—
by_soc_pt	statistic	Placebo vs. Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hypothesis_test	p_value_fmt	Fisher's exact p-value (formatted)	—	—
by_soc_pt	statistic	Placebo vs. High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hypothesis_test	p_value	Fisher's exact p-value	—	—	0.494117647058824
by_soc_pt	statistic	Placebo vs. High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	PARTIAL SEIZURES WITH SECONDARY GENERALISATION	hypothesis_test	p_value_fmt	Fisher's exact p-value (formatted)	—	—	0.494
by_soc_pt	TRT01A	Placebo	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	n	n	—	—	0
by_soc_pt	TRT01A	Placebo	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	N	N	—	—	86
by_soc_pt	TRT01A	Placebo	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	p	%	—	—	0
by_soc_pt	TRT01A	Placebo	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	events	Events	—	—	0
by_soc_pt	TRT01A	Xanomeline Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	n	n	—	—	1
by_soc_pt	TRT01A	Xanomeline Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	N	N	—	—	84
by_soc_pt	TRT01A	Xanomeline Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	p	%	—	—	0.0119047619047619
by_soc_pt	TRT01A	Xanomeline Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	events	Events	—	—	1
by_soc_pt	TRT01A	Xanomeline High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	n	n	—	—	1
by_soc_pt	TRT01A	Xanomeline High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	N	N	—	—	84
by_soc_pt	TRT01A	Xanomeline High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	p	%	—	—	0.0119047619047619
by_soc_pt	TRT01A	Xanomeline High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hierarchical	events	Events	—	—	1
by_soc_pt	statistic	Placebo vs. Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hypothesis_test	p_value	Fisher's exact p-value	—	—	0.494117647058824
by_soc_pt	statistic	Placebo vs. Low Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hypothesis_test	p_value_fmt	Fisher's exact p-value (formatted)	—	—	0.494
by_soc_pt	statistic	Placebo vs. High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hypothesis_test	p_value	Fisher's exact p-value	—	—	0.494117647058824
by_soc_pt	statistic	Placebo vs. High Dose	AEBODSYS	NERVOUS SYSTEM DISORDERS	AEDECOD	SYNCOPE	hypothesis_test	p_value_fmt	Fisher's exact p-value (formatted)	—	—	0.494

64 rows, one per computed statistic.

Schema: opencsr/ard/v1
Generated: 2026-09-02T16:02:57Z
Spec hash: sha256:065d87f5040a5927a3927158a61b168fcd2f60725b9afdc25057beaa22a83a4e
Display hash: sha256:2e8296c3061f15bfb06c8eb0228fab6917e7c48fddd0086f357c87afd039b1a8
ARD file: outputs/t-sae-incidence/v006/ard.json
ARD hash: sha256:94a983c62001c7f8ecdb7e411c6fbb7a9cdff8a5fab2f0597a4c38f3f8a3c0ca

Source datasets

Dataset	Rows	Package	Hash
adsl	254	phuse-org/phuse-scripts:data/adam 398a6d33ced9359ffb58c46650a6d488811176b1	sha256:3139478d86fda4c38e8bb2f41d348518f4a65f58bcdd7e9650fda8da7a9a6838
adae	1191	phuse-org/phuse-scripts:data/adam 398a6d33ced9359ffb58c46650a6d488811176b1	sha256:4ffe4e4c90c8a531e95e4931b601c258ed0b83638d4b346e66635d79e78a7bf1

Environment

R 4.3.3 · Darwin 23.6.0 · cards 0.6.1 · cardx 0.2.5 · gtsummary 2.3.0 · gt 1.0.0 · dplyr 1.1.4 · pharmaverseadam 1.1.0 · jsonlite 2.0.0 · yaml 2.3.10 · digest 0.6.37

library/tfl/t-sae-incidence/analysis.yaml

# ------------------------------------------------------------------------------
# t-sae-incidence — Incidence of Treatment Emergent Serious Adverse Events by Treatment Group
# ------------------------------------------------------------------------------
# Target: Table 14-5.02 of the CDISCPILOT01 clinical study report (27 June 2006).
# The same statistics and tests as t-ae-incidence, on the treatment-emergent
# events flagged serious. The functions are t-ae-incidence's, sourced through
# `custom_from`, so the two tables cannot drift apart in how they count.
# ------------------------------------------------------------------------------
id: t-sae-incidence
title: "Incidence of Treatment Emergent Serious Adverse Events by Treatment Group"
regulatory_id: AET04
type: table
dataset: adae
analysis_set: safety
denominator: adsl
custom_from: t-ae-incidence
group:
  - TRT01A
total: false
analyses:
  - name: any
    method: subject_count
    custom: ard_incidence_any
    reference_arm: Placebo
    label: "Any body system"
    variable: AEDECOD
    filter: "TRTEMFL == 'Y' & AESER == 'Y'"
  - name: by_soc_pt
    method: hierarchical_count
    custom: ard_incidence_hierarchy
    reference_arm: Placebo
    label: "Serious adverse events by system organ class and preferred term"
    hierarchy: [AEBODSYS, AEDECOD]
    filter: "TRTEMFL == 'Y' & AESER == 'Y'"

library/tfl/t-sae-incidence/display.yaml

id: t-sae-incidence
title: "Incidence of Treatment Emergent Serious Adverse Events by Treatment Group"
study: CDISCPILOT01
population_label: "Safety Analysis Set"
cutoff: "2014-07-01"
source: "Source: adae, adsl (CDISCPILOT01 ADaM package, phuse-org/phuse-scripts). Data cut-off: 2014-07-01."
footnotes:
  - "Serious treatment-emergent events are those flagged AESER = 'Y' and TRTEMFL = 'Y' in the study's ADAE, as the reference report (Table 14-5.02) counts them. Adverse events are coded using MedDRA."
  - "Subjects are counted once per system organ class and once per preferred term; percentages are based on the number of subjects in the safety population within each treatment group. The bracketed figure is the total number of times an event was recorded."
  - "P-values are Fisher's exact test comparing placebo with each active treatment group on the number of subjects with the event. An asterisk is appended to p-values below 0.15, as in the reference report; a p-value that rounds to 1 prints as >0.99; where neither arm has a subject with the event there is no test and the cell is blank."
  - "System organ classes are in alphabetical order; preferred terms within a class are in descending order of subjects across the three groups, then alphabetical — the order the reference report's serious-events program prints, which differs from its full incidence table."
columns:
  order: [Placebo, "Xanomeline Low Dose", "Xanomeline High Dose", "Placebo vs. Low Dose", "Placebo vs. High Dose"]
  patterns:
    "Placebo vs. Low Dose": pvalue
    "Placebo vs. High Dose": pvalue
format:
  n_pct_events: "{n} ({p}%) [{events}]"
  pvalue: "{p_value_fmt}"
  zero_count: "0"
  digits:
    p: 1
    events: 0
rows:
  - { analysis: any, label: "ANY BODY SYSTEM", pattern: n_pct_events, indent: 0 }
  - analysis: by_soc_pt
    type: hierarchical
    levels: [AEBODSYS, AEDECOD]
    pattern: n_pct_events
    sort:
      outer: alpha
      inner: { by: sum }
variants:
  post_text: {}
  in_text:
    title: "Serious Adverse Events (Summary)"

Every iteration is kept: outputs/t-sae-incidence/vNNN/ holds the spec snapshot, the ARD, the rendered output, and a manifest recording who regenerated it, why, and from which commit.